From 1f7fca8e49ec1a089ba6a06a9ce9ebc820afc04b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 20 Mar 2007 11:41:12 +0000
Subject: [PATCH] Update Vega parser to be more generic.
---
.../xref_mapping/XrefParser/VegaParser.pm | 35 +++++++++----------
1 file changed, 16 insertions(+), 19 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaParser.pm
index e27e896791..314a0911ea 100644
--- a/misc-scripts/xref_mapping/XrefParser/VegaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VegaParser.pm
@@ -7,7 +7,12 @@ use strict;
use base qw( XrefParser::BaseParser );
-# Parses the Vega Fasta file format:
+# Parses the Vega CDNA and Peptide Fasta file format:
+#
+# >OTTMUST00000004500 cdna:tot chromosome:VEGA:1:60690948:60709172:1 Gene:OTTMUSG00000002254
+# GTGACTTCAGTTCACACCACACTCTGCCTTGCTCACAGAGGAGGGGCTGCAGCCCTGGCC
+# CTCATCAGAACAATGACACTCAGGCTGCTGTTCTTGGCTCTCAACTTCTTCTCAGTTCAA
+# GTAACAGAAAACAAGATTTTGGTAAAGCAGTCGCCCCTGCTTGTGGTAGATAGCAACGAG
#
# >OTTMUSP00000002157 pep:known chromosome:VEGA:1:60690904:60717905:1 Gene:OTTMUSG00000002254 Transcript:OTTMUST00000004499
# MTLRLLFLALNFFSVQVTENKILVKQSPLLVVDSNEVSLSCRYSYNLLAKEFRASLYKGV
@@ -32,30 +37,22 @@ sub run
if ( substr( $line, 0, 1 ) eq '>' ) {
# New sequence header.
- my (
- $vega_protein_id, $vega_type,
- $vega_position, $vega_gene_id,
- $vega_transcript_id
- ) = split / /, $line;
- substr( $vega_protein_id, 0, 1, '' ); # Remove initial '>',
- substr( $vega_gene_id, 0, 5, '' ); # initial 'Gene:', and
- substr( $vega_transcript_id, 0, 11, '' ); # 'Transcript:'.
+ substr( $line, 0, 1, '' ); # Remove initial '>'
- my ( $vega_alphabet, $vega_status ) =
- ( $vega_type =~ /(.*):(.*)/ );
+ my ( $vega_id, $vega_alphabet ) =
+ ( $line =~ /^(\S+)\s([^:]+):/ );
my %xref = (
- 'ACCESSION' => $vega_transcript_id,
- 'LABEL' => $vega_transcript_id,
- 'DESCRIPTION' =>
- sprintf( "%s %s", $vega_type, $vega_position ),
- 'SEQUENCE' => '',
- 'SOURCE_ID' => $source_id,
- 'SPECIES_ID' => $species_id,
+ 'ACCESSION' => $vega_id,
+ 'LABEL' => $vega_id,
+ 'DESCRIPTION' => $line,
+ 'SEQUENCE' => '',
+ 'SOURCE_ID' => $source_id,
+ 'SPECIES_ID' => $species_id,
'SEQUENCE_TYPE' =>
( $vega_alphabet eq 'pep' ? 'peptide' : 'dna' ),
- 'STATUS' => $vega_status,
+ 'STATUS' => 'experimental'
);
push @xrefs, \%xref;
--
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